Publikationsliste
“VANILLA: Validated knowledge graph completion—A Normalization-based framework for Integrity, Link prediction, and Logical Accuracy”
September 2025
Knowledge-Based Systems, 325, Article 113939
CAIMed Groups:
AI & Active Agents
Semantic Models
Knowledge graphs (KGs) are expressive data structures for integrating and describing heterogeneous data by unifying factual information and domain knowledge. However, under the Open World Assumption (OWA), the absence of facts does not imply falsity—only incompleteness. Inductive learning methods, particularly numerical techniques such as Knowledge Graph Embeddings (KGEs) and Graph Neural Networks (GNNs), are widely used for link prediction and classification tasks in KGs. These models excel at capturing latent patterns and exploiting structural properties at scale. Nevertheless, their performance can be significantly degraded by anomalies in KG representations—semantic inconsistencies and modeling artifacts that arise from unconstrained data integration. Such anomalies obscure the intended meaning of relations, introduce noise, and mislead numerical learning models. To address this issue, we introduce a normalization theory for KGs that enforces semantic consistency through normal forms. These forms restructure KGs to eliminate representational anomalies, ensuring that the data adheres to well-defined semantic constraints. We present VANILLA, a neuro-symbolic framework that combines symbolic rule learning, numerical inductive models, and constraint-based validation. By aligning inductive predictions with normalized, ontology-aware KG structures, VANILLA enables accurate and semantically grounded KG completion. Experimental results show that our approach significantly improves predictive performance while maintaining semantic integrity, demonstrating the value of normalization in hybrid KG learning systems. VANILLA is publicly available on GitHub https://github.com/SDM-TIB/VANILLA
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Funded by CAIMed
“A rule-based clinical decision support system for detection of acute kidney injury after pediatric cardiac surgery”
July 2025
Computers in Biology and Medicine, 193, 110382
Janice Wachenbrunner, Marcel Mast, Julia Böhnke, Nicole Rübsamen, Louisa Bode, André Karch, Henning Rathert, Alexander Horke, Philipp Beerbaum, Michael Marschollek, Thomas Jack, Martin Böhne
CAIMed Groups:
AI & Decisions
Clinical Decision Support
Acute kidney injury (AKI) is common in children with congenital heart disease following open-heart surgery with cardiopulmonary bypass (CPB). Early AKI detection in critically ill children requires clinician expertise to compile various data from different sources within a stressful and time-sensitive environment. However, as electronic health records provide data in a machine-readable format, this process could be supported by computerized systems. Therefore, we developed a time-aware, rule-based clinical decision support system (CDSS) to detect, stage, and track temporal AKI progression in children.
Der vollständige Text ist here zu finden.
Funded by CAIMed
“Transient silencing of hypermutation preserves B cell affinity during clonal bursting”
March 2025
Nature 641, 486–494
Juhee Pae, Niklas Schwan, Bertrand Ottino-Loffler, William S. DeWitt, Amar Garg, Juliana Bortolatto, Ashni A. Vora, Jin-Jie Shen, Alvaro Hobbs, Tiago B. R. Castro, Luka Mesin, Frederick A. Matsen IV, Michael Meyer-Hermann & Gabriel D. Victora
CAIMed Groups:
AI & Active Agents
Mathematical Models
In the course of antibody affinity maturation, germinal centre (GC) B cells mutate their immunoglobulin heavy- and light-chain genes in a process known as somatic hypermutation (SHM). Panels of mutant B cells with different binding affinities for antigens are then selected in a Darwinian manner, which leads to a progressive increase in affinity among the population. As with any Darwinian process, rare gain-of-fitness mutations must be identified and common loss-of-fitness mutations avoided. Progressive acquisition of mutations therefore poses a risk during large proliferative bursts, when GC B cells undergo several cell cycles in the absence of affinity-based selection. Using a combination of in vivo mouse experiments and mathematical modelling, here we show that GCs achieve this balance by strongly suppressing SHM during clonal-burst-type expansion, so that a large fraction of the progeny generated by these bursts does not deviate from their ancestral genotype. Intravital imaging and image-based cell sorting of a mouse strain carrying a reporter of cyclin-dependent kinase 2 (CDK2) activity showed that B cells that are actively undergoing proliferative bursts lack the transient CDK2low ‘G0-like’ phase of the cell cycle in which SHM takes place. We propose a model in which inertially cycling B cells mostly delay SHM until the G0-like phase that follows their final round of division in the GC dark zone, thus maintaining affinity as they clonally expand in the absence of selection.
Der vollständige Text ist here zu finden.
Funded by CAIMed
Preprints
“Auto-nnU-Net: Towards Automated Medical Image Segmentation”
22 May 2025 (submission date)
arxiv.org
CAIMed Groups:
AI & Decision
Human-Centered AI
Medical Image Segmentation (MIS) includes diverse tasks, from bone to organ segmentation, each with its own challenges in finding the best segmentation model. The state-of-the-art AutoML-related MIS-framework nnU-Net automates many aspects of model configuration but remains constrained by fixed hyperparameters and heuristic design choices. As a full-AutoML framework for MIS, we propose Auto-nnU-Net, a novel nnU-Net variant enabling hyperparameter optimization (HPO), neural architecture search (NAS), and hierarchical NAS (HNAS). Additionally, we propose Regularized PriorBand to balance model accuracy with the computational resources required for training, addressing the resource constraints often faced in real-world medical settings that limit the feasibility of extensive training procedures. We evaluate our approach across diverse MIS datasets from the well-established Medical Segmentation Decathlon, analyzing the impact of AutoML techniques on segmentation performance, computational efficiency, and model design choices. The results demonstrate that our AutoML approach substantially improves the segmentation performance of nnU-Net on 6 out of 10 datasets and is on par on the other datasets while maintaining practical resource requirements. Our code is available at this URL.
Der vollständige Text ist here zu finden.
Funded by CAIMed